[gmx-users] Regarding calculation of Hydrogen-Bond

[Erik Marklund]

The point is that Calpha don’t form hydrogen bonds.

Erik
______________________________________________
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>

On 13 Mar 2018, at 13:20, Dilip H N <cy16f01.dilip at nitk.edu.in<mailto:cy16f01.dilip at nitk.edu.in>> wrote:

Then how can i calculate the hydrogen bonding between C-alpha and Oxygen
atom of water molecules..??
What are the other possible ways..??



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On Tue, Mar 13, 2018 at 4:12 PM, Erik Marklund <erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se>>
wrote:

Dear Dilip,

The Calpha is not considered a hbond donor.

Kind regards,
Erik
______________________________________________
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4539
erik.marklund at kemi.uu.se<mailto:erik.marklund at kemi.uu.se><mailto:erik.marklund at kemi.uu.se>

On 13 Mar 2018, at 11:03, Dilip H N <cy16f01.dilip at nitk.edu.in<mailto:cy16f01.dilip at nitk.edu.in><mailto:
cy16f01.dilip at nitk.edu.in<mailto:cy16f01.dilip at nitk.edu.in>>> wrote:

Hello,
I want to calculate Hydrogen bonding between C-alpha of glycine and the
oxygen atom of water molecules.
So, i gave the command as:-

gmx hbond -f nptmd.trr -s nptmd.tpr -n CaOw.ndx -num abc.xvg

but i got the error as:
Calculating hydrogen bonds between OW (511 atoms) and CA (1 atoms)
Found 0 donors and 511 acceptors
No Donors found
-------------------------------------------------------
Program:     gmx hbond, version 2016.2
Source file: src/gromacs/gmxana/gmx_hbond.cpp (line 2732)
Fatal error:
Nothing to be done

So, how can i solve this issue..?? Is there no any Hydrogen bonding between
this..?? (I think there is some hydrogen bonding present ...)

Any suggestions are appreciated.

Thank you.

--
With Best Regards,

DILIP.H.N
PhD Student



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With Best Regards,

DILIP.H.N
Ph.D Student
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